[2014-04-30 05:14:17] Beginning TopHat run (v2.0.8b)
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[2014-04-30 05:14:17] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 05:14:17] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 05:14:17] Checking for Bowtie index files
[2014-04-30 05:14:17] Checking for reference FASTA file
[2014-04-30 05:14:17] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 05:14:19] Preparing reads
	 left reads: min. length=60, max. length=101, 19755802 kept reads (10312 discarded)
[2014-04-30 05:22:24] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 05:47:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 05:49:27] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 05:51:36] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 05:54:03] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 05:56:36] Searching for junctions via segment mapping
[2014-04-30 06:01:24] Retrieving sequences for splices
[2014-04-30 06:03:21] Indexing splices
[2014-04-30 06:03:59] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 06:04:54] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 06:06:00] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 06:07:06] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 06:08:10] Joining segment hits
[2014-04-30 06:11:27] Reporting output tracks
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[2014-04-30 06:23:19] Run complete: 01:09:02 elapsed